Starting phenix.real_space_refine on Mon Jul 6 10:26:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rlf_24528/07_2026/7rlf_24528.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rlf_24528/07_2026/7rlf_24528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7rlf_24528/07_2026/7rlf_24528.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rlf_24528/07_2026/7rlf_24528.cif" model { file = "/net/cci-nas-00/data/ceres_data/7rlf_24528/07_2026/7rlf_24528.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rlf_24528/07_2026/7rlf_24528.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rlf_24528/07_2026/7rlf_24528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rlf_24528/07_2026/7rlf_24528.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 12 5.21 5 S 192 5.16 5 C 21630 2.51 5 N 6090 2.21 5 O 6618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34578 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5699 Classifications: {'peptide': 728} Link IDs: {'PCIS': 2, 'PTRANS': 37, 'TRANS': 688} Chain breaks: 1 Chain: "B" Number of atoms: 5699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5699 Classifications: {'peptide': 728} Link IDs: {'PCIS': 2, 'PTRANS': 37, 'TRANS': 688} Chain breaks: 1 Chain: "C" Number of atoms: 5699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5699 Classifications: {'peptide': 728} Link IDs: {'PCIS': 2, 'PTRANS': 37, 'TRANS': 688} Chain breaks: 1 Chain: "D" Number of atoms: 5699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5699 Classifications: {'peptide': 728} Link IDs: {'PCIS': 2, 'PTRANS': 37, 'TRANS': 688} Chain breaks: 1 Chain: "E" Number of atoms: 5699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5699 Classifications: {'peptide': 728} Link IDs: {'PCIS': 2, 'PTRANS': 37, 'TRANS': 688} Chain breaks: 1 Chain: "F" Number of atoms: 5699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5699 Classifications: {'peptide': 728} Link IDs: {'PCIS': 2, 'PTRANS': 37, 'TRANS': 688} Chain breaks: 1 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 6.78, per 1000 atoms: 0.20 Number of scatterers: 34578 At special positions: 0 Unit cell: (169.113, 175.338, 98.5625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 192 16.00 P 36 15.00 Mg 12 11.99 O 6618 8.00 N 6090 7.00 C 21630 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 1.4 seconds 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8148 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 24 sheets defined 48.6% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 42 through 49 removed outlier: 3.825A pdb=" N MET A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 90 removed outlier: 4.058A pdb=" N ASN A 90 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 135 through 140 removed outlier: 3.855A pdb=" N LEU A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 210 through 226 removed outlier: 4.993A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 226 through 234 Processing helix chain 'A' and resid 250 through 261 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 281 through 296 Processing helix chain 'A' and resid 305 through 310 removed outlier: 4.137A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 334 removed outlier: 3.608A pdb=" N ARG A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 339 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.694A pdb=" N ARG A 359 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 386 Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 407 through 425 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.582A pdb=" N MET A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 458 Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 499 removed outlier: 4.029A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.794A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 536 Processing helix chain 'A' and resid 544 through 552 Processing helix chain 'A' and resid 556 through 569 removed outlier: 3.823A pdb=" N ARG A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 584 removed outlier: 3.982A pdb=" N ILE A 582 " --> pdb=" O GLU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 610 removed outlier: 3.929A pdb=" N GLN A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 Processing helix chain 'A' and resid 649 through 661 Processing helix chain 'A' and resid 671 through 679 Processing helix chain 'A' and resid 683 through 707 Processing helix chain 'A' and resid 732 through 742 removed outlier: 3.603A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 761 Processing helix chain 'B' and resid 42 through 49 removed outlier: 3.824A pdb=" N MET B 46 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP B 47 " --> pdb=" O GLN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 90 removed outlier: 4.057A pdb=" N ASN B 90 " --> pdb=" O ARG B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 135 Processing helix chain 'B' and resid 135 through 140 removed outlier: 3.854A pdb=" N LEU B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 210 through 226 removed outlier: 4.992A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 234 Processing helix chain 'B' and resid 250 through 261 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 281 through 296 Processing helix chain 'B' and resid 305 through 310 removed outlier: 4.137A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 334 removed outlier: 3.606A pdb=" N ARG B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 339 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.695A pdb=" N ARG B 359 " --> pdb=" O ALA B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 386 Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 407 through 425 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.582A pdb=" N MET B 442 " --> pdb=" O ASP B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 458 Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 499 removed outlier: 4.028A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 499 through 507 removed outlier: 3.793A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 536 Processing helix chain 'B' and resid 544 through 552 Processing helix chain 'B' and resid 556 through 569 removed outlier: 3.824A pdb=" N ARG B 560 " --> pdb=" O GLU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 584 removed outlier: 3.982A pdb=" N ILE B 582 " --> pdb=" O GLU B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 610 removed outlier: 3.928A pdb=" N GLN B 603 " --> pdb=" O ARG B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 649 through 661 Processing helix chain 'B' and resid 671 through 679 Processing helix chain 'B' and resid 683 through 707 Processing helix chain 'B' and resid 732 through 742 removed outlier: 3.603A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 761 Processing helix chain 'C' and resid 42 through 49 removed outlier: 3.824A pdb=" N MET C 46 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP C 47 " --> pdb=" O GLN C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 90 removed outlier: 4.058A pdb=" N ASN C 90 " --> pdb=" O ARG C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 135 Processing helix chain 'C' and resid 135 through 140 removed outlier: 3.854A pdb=" N LEU C 140 " --> pdb=" O LYS C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 210 through 226 removed outlier: 4.993A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 226 through 234 Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 281 through 296 Processing helix chain 'C' and resid 305 through 310 removed outlier: 4.137A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 334 removed outlier: 3.607A pdb=" N ARG C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 339 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 354 through 359 removed outlier: 3.693A pdb=" N ARG C 359 " --> pdb=" O ALA C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 386 Processing helix chain 'C' and resid 395 through 403 Processing helix chain 'C' and resid 407 through 425 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.581A pdb=" N MET C 442 " --> pdb=" O ASP C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 458 Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 499 removed outlier: 4.029A pdb=" N TYR C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.795A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 536 Processing helix chain 'C' and resid 544 through 552 Processing helix chain 'C' and resid 556 through 569 removed outlier: 3.823A pdb=" N ARG C 560 " --> pdb=" O GLU C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 584 removed outlier: 3.982A pdb=" N ILE C 582 " --> pdb=" O GLU C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 610 removed outlier: 3.929A pdb=" N GLN C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 635 Processing helix chain 'C' and resid 649 through 661 Processing helix chain 'C' and resid 671 through 679 Processing helix chain 'C' and resid 683 through 707 Processing helix chain 'C' and resid 732 through 742 removed outlier: 3.603A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 761 Processing helix chain 'D' and resid 42 through 49 removed outlier: 3.824A pdb=" N MET D 46 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP D 47 " --> pdb=" O GLN D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 90 removed outlier: 4.058A pdb=" N ASN D 90 " --> pdb=" O ARG D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 135 Processing helix chain 'D' and resid 135 through 140 removed outlier: 3.854A pdb=" N LEU D 140 " --> pdb=" O LYS D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 210 through 226 removed outlier: 4.993A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 234 Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 281 through 296 Processing helix chain 'D' and resid 305 through 310 removed outlier: 4.138A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 334 removed outlier: 3.607A pdb=" N ARG D 322 " --> pdb=" O GLY D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 339 Processing helix chain 'D' and resid 349 through 353 Processing helix chain 'D' and resid 354 through 359 removed outlier: 3.693A pdb=" N ARG D 359 " --> pdb=" O ALA D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 386 Processing helix chain 'D' and resid 395 through 403 Processing helix chain 'D' and resid 407 through 425 Processing helix chain 'D' and resid 438 through 443 removed outlier: 3.583A pdb=" N MET D 442 " --> pdb=" O ASP D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 458 Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 499 removed outlier: 4.028A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 499 through 507 removed outlier: 3.794A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 536 Processing helix chain 'D' and resid 544 through 552 Processing helix chain 'D' and resid 556 through 569 removed outlier: 3.823A pdb=" N ARG D 560 " --> pdb=" O GLU D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 584 removed outlier: 3.982A pdb=" N ILE D 582 " --> pdb=" O GLU D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 610 removed outlier: 3.929A pdb=" N GLN D 603 " --> pdb=" O ARG D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 635 Processing helix chain 'D' and resid 649 through 661 Processing helix chain 'D' and resid 671 through 679 Processing helix chain 'D' and resid 683 through 707 Processing helix chain 'D' and resid 732 through 742 removed outlier: 3.603A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 761 Processing helix chain 'E' and resid 42 through 49 removed outlier: 3.824A pdb=" N MET E 46 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP E 47 " --> pdb=" O GLN E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 90 removed outlier: 4.058A pdb=" N ASN E 90 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 135 Processing helix chain 'E' and resid 135 through 140 removed outlier: 3.854A pdb=" N LEU E 140 " --> pdb=" O LYS E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 210 through 226 removed outlier: 4.993A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 226 through 234 Processing helix chain 'E' and resid 250 through 261 Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 281 through 296 Processing helix chain 'E' and resid 305 through 310 removed outlier: 4.136A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 334 removed outlier: 3.606A pdb=" N ARG E 322 " --> pdb=" O GLY E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 339 Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 354 through 359 removed outlier: 3.694A pdb=" N ARG E 359 " --> pdb=" O ALA E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 386 Processing helix chain 'E' and resid 395 through 403 Processing helix chain 'E' and resid 407 through 425 Processing helix chain 'E' and resid 438 through 443 removed outlier: 3.582A pdb=" N MET E 442 " --> pdb=" O ASP E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 458 Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 499 removed outlier: 4.029A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 499 through 507 removed outlier: 3.794A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 536 Processing helix chain 'E' and resid 544 through 552 Processing helix chain 'E' and resid 556 through 569 removed outlier: 3.824A pdb=" N ARG E 560 " --> pdb=" O GLU E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 578 through 584 removed outlier: 3.982A pdb=" N ILE E 582 " --> pdb=" O GLU E 578 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 610 removed outlier: 3.929A pdb=" N GLN E 603 " --> pdb=" O ARG E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 635 Processing helix chain 'E' and resid 649 through 661 Processing helix chain 'E' and resid 671 through 679 Processing helix chain 'E' and resid 683 through 707 Processing helix chain 'E' and resid 732 through 742 removed outlier: 3.602A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 761 Processing helix chain 'F' and resid 42 through 49 removed outlier: 3.824A pdb=" N MET F 46 " --> pdb=" O SER F 42 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP F 47 " --> pdb=" O GLN F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 90 removed outlier: 4.058A pdb=" N ASN F 90 " --> pdb=" O ARG F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 135 Processing helix chain 'F' and resid 135 through 140 removed outlier: 3.854A pdb=" N LEU F 140 " --> pdb=" O LYS F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 210 through 226 removed outlier: 4.993A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 226 through 234 Processing helix chain 'F' and resid 250 through 261 Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 281 through 296 Processing helix chain 'F' and resid 305 through 310 removed outlier: 4.137A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 334 removed outlier: 3.607A pdb=" N ARG F 322 " --> pdb=" O GLY F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 339 Processing helix chain 'F' and resid 349 through 353 Processing helix chain 'F' and resid 354 through 359 removed outlier: 3.694A pdb=" N ARG F 359 " --> pdb=" O ALA F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 386 Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 407 through 425 Processing helix chain 'F' and resid 438 through 443 removed outlier: 3.582A pdb=" N MET F 442 " --> pdb=" O ASP F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 458 Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 499 removed outlier: 4.030A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 507 removed outlier: 3.794A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 536 Processing helix chain 'F' and resid 544 through 552 Processing helix chain 'F' and resid 556 through 569 removed outlier: 3.823A pdb=" N ARG F 560 " --> pdb=" O GLU F 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 578 through 584 removed outlier: 3.982A pdb=" N ILE F 582 " --> pdb=" O GLU F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 610 removed outlier: 3.928A pdb=" N GLN F 603 " --> pdb=" O ARG F 599 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 635 Processing helix chain 'F' and resid 649 through 661 Processing helix chain 'F' and resid 671 through 679 Processing helix chain 'F' and resid 683 through 707 Processing helix chain 'F' and resid 732 through 742 removed outlier: 3.603A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 761 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 27 Processing sheet with id=AA2, first strand: chain 'A' and resid 114 through 118 removed outlier: 6.838A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.294A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL A 367 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU A 242 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 543 removed outlier: 6.558A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 25 through 27 Processing sheet with id=AA6, first strand: chain 'B' and resid 114 through 118 removed outlier: 6.837A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.294A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 538 through 543 removed outlier: 6.558A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASP B 577 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE B 542 " --> pdb=" O ASP B 577 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 25 through 27 Processing sheet with id=AB1, first strand: chain 'C' and resid 114 through 118 removed outlier: 6.837A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.294A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL C 367 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 538 through 543 removed outlier: 6.558A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASP C 577 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE C 542 " --> pdb=" O ASP C 577 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 25 through 27 Processing sheet with id=AB5, first strand: chain 'D' and resid 114 through 118 removed outlier: 6.838A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.293A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL D 367 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 538 through 543 removed outlier: 6.558A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASP D 577 " --> pdb=" O ILE D 540 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE D 542 " --> pdb=" O ASP D 577 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 25 through 27 Processing sheet with id=AB9, first strand: chain 'E' and resid 114 through 118 removed outlier: 6.838A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.294A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL E 367 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 538 through 543 removed outlier: 6.558A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASP E 577 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE E 542 " --> pdb=" O ASP E 577 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 25 through 27 Processing sheet with id=AC4, first strand: chain 'F' and resid 114 through 118 removed outlier: 6.838A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 265 through 270 removed outlier: 6.293A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL F 367 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU F 242 " --> pdb=" O VAL F 367 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 538 through 543 removed outlier: 6.559A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASP F 577 " --> pdb=" O ILE F 540 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE F 542 " --> pdb=" O ASP F 577 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) 1464 hydrogen bonds defined for protein. 4176 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.52 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 11947 1.37 - 1.51: 9625 1.51 - 1.66: 13276 1.66 - 1.80: 211 1.80 - 1.95: 89 Bond restraints: 35148 Sorted by residual: bond pdb=" CD ARG A 225 " pdb=" NE ARG A 225 " ideal model delta sigma weight residual 1.458 1.481 -0.023 1.40e-02 5.10e+03 2.62e+00 bond pdb=" CD ARG D 113 " pdb=" NE ARG D 113 " ideal model delta sigma weight residual 1.458 1.481 -0.023 1.40e-02 5.10e+03 2.60e+00 bond pdb=" CD ARG E 225 " pdb=" NE ARG E 225 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.40e-02 5.10e+03 2.58e+00 bond pdb=" CD ARG C 225 " pdb=" NE ARG C 225 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.40e-02 5.10e+03 2.55e+00 bond pdb=" CD ARG F 113 " pdb=" NE ARG F 113 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.40e-02 5.10e+03 2.50e+00 ... (remaining 35143 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 46288 1.50 - 3.01: 1014 3.01 - 4.51: 187 4.51 - 6.01: 49 6.01 - 7.52: 12 Bond angle restraints: 47550 Sorted by residual: angle pdb=" N ASP D 121 " pdb=" CA ASP D 121 " pdb=" C ASP D 121 " ideal model delta sigma weight residual 114.56 108.72 5.84 1.27e+00 6.20e-01 2.12e+01 angle pdb=" N ASP A 121 " pdb=" CA ASP A 121 " pdb=" C ASP A 121 " ideal model delta sigma weight residual 114.56 108.72 5.84 1.27e+00 6.20e-01 2.12e+01 angle pdb=" N ASP E 121 " pdb=" CA ASP E 121 " pdb=" C ASP E 121 " ideal model delta sigma weight residual 114.56 108.72 5.84 1.27e+00 6.20e-01 2.11e+01 angle pdb=" N ASP B 121 " pdb=" CA ASP B 121 " pdb=" C ASP B 121 " ideal model delta sigma weight residual 114.56 108.75 5.81 1.27e+00 6.20e-01 2.10e+01 angle pdb=" N ASP F 121 " pdb=" CA ASP F 121 " pdb=" C ASP F 121 " ideal model delta sigma weight residual 114.56 108.75 5.81 1.27e+00 6.20e-01 2.10e+01 ... (remaining 47545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.22: 19271 16.22 - 32.45: 1727 32.45 - 48.67: 506 48.67 - 64.89: 132 64.89 - 81.12: 60 Dihedral angle restraints: 21696 sinusoidal: 9126 harmonic: 12570 Sorted by residual: dihedral pdb=" CA ALA E 297 " pdb=" C ALA E 297 " pdb=" N PRO E 298 " pdb=" CA PRO E 298 " ideal model delta harmonic sigma weight residual 180.00 162.11 17.89 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA ALA D 297 " pdb=" C ALA D 297 " pdb=" N PRO D 298 " pdb=" CA PRO D 298 " ideal model delta harmonic sigma weight residual 180.00 162.12 17.88 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA ALA B 297 " pdb=" C ALA B 297 " pdb=" N PRO B 298 " pdb=" CA PRO B 298 " ideal model delta harmonic sigma weight residual 180.00 162.13 17.87 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 21693 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2908 0.026 - 0.052: 1408 0.052 - 0.078: 556 0.078 - 0.104: 341 0.104 - 0.130: 151 Chirality restraints: 5364 Sorted by residual: chirality pdb=" CA ILE A 371 " pdb=" N ILE A 371 " pdb=" C ILE A 371 " pdb=" CB ILE A 371 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA ILE C 371 " pdb=" N ILE C 371 " pdb=" C ILE C 371 " pdb=" CB ILE C 371 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CA ILE B 371 " pdb=" N ILE B 371 " pdb=" C ILE B 371 " pdb=" CB ILE B 371 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 ... (remaining 5361 not shown) Planarity restraints: 6234 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 297 " 0.036 5.00e-02 4.00e+02 5.47e-02 4.79e+00 pdb=" N PRO A 298 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 298 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 298 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 297 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.71e+00 pdb=" N PRO B 298 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 298 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 298 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 297 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.71e+00 pdb=" N PRO D 298 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 298 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 298 " -0.030 5.00e-02 4.00e+02 ... (remaining 6231 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 445 2.61 - 3.18: 30553 3.18 - 3.76: 55294 3.76 - 4.33: 75297 4.33 - 4.90: 122098 Nonbonded interactions: 283687 Sorted by model distance: nonbonded pdb=" OG1 THR A 525 " pdb="MG MG A 904 " model vdw 2.042 2.170 nonbonded pdb=" OG1 THR C 525 " pdb="MG MG C 904 " model vdw 2.042 2.170 nonbonded pdb=" OG1 THR B 525 " pdb="MG MG B 904 " model vdw 2.043 2.170 nonbonded pdb=" OG1 THR F 525 " pdb="MG MG F 904 " model vdw 2.043 2.170 nonbonded pdb=" OG1 THR E 525 " pdb="MG MG E 904 " model vdw 2.043 2.170 ... (remaining 283682 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 30.960 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.890 35154 Z= 1.042 Angle : 0.577 7.519 47550 Z= 0.322 Chirality : 0.043 0.130 5364 Planarity : 0.004 0.055 6234 Dihedral : 14.612 81.118 13548 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.87 % Favored : 95.86 % Rotamer: Outliers : 0.19 % Allowed : 14.11 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.14), residues: 4344 helix: 1.20 (0.13), residues: 1854 sheet: 0.28 (0.21), residues: 636 loop : -0.48 (0.16), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 766 TYR 0.012 0.001 TYR E 138 PHE 0.009 0.001 PHE F 736 TRP 0.008 0.001 TRP E 551 HIS 0.005 0.001 HIS E 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (35148) covalent geometry : angle 0.57728 / 0.32 (47550) hydrogen bonds : bond 0.18224 / 12.20 ( 1464) hydrogen bonds : angle 5.89656 / 4.24 ( 4176) Misc. bond : bond 0.78784 / 38.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 229 time to evaluate : 1.267 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.6033 (tpt) cc_final: 0.5826 (tpt) REVERT: A 230 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.8534 (t80) REVERT: A 236 LYS cc_start: 0.8824 (mmmt) cc_final: 0.8604 (mmtm) REVERT: B 84 MET cc_start: 0.5722 (tpt) cc_final: 0.5401 (tpt) REVERT: B 344 MET cc_start: 0.8851 (mtp) cc_final: 0.8548 (ttm) REVERT: B 420 LEU cc_start: 0.8813 (mt) cc_final: 0.8570 (mt) REVERT: B 449 MET cc_start: 0.8843 (tpt) cc_final: 0.7984 (tpp) REVERT: C 84 MET cc_start: 0.5027 (tpt) cc_final: 0.4813 (tpt) REVERT: C 158 MET cc_start: 0.9254 (ttm) cc_final: 0.9030 (ttp) REVERT: D 84 MET cc_start: 0.6025 (tpt) cc_final: 0.5780 (tpt) REVERT: D 230 PHE cc_start: 0.9010 (OUTLIER) cc_final: 0.8527 (t80) REVERT: E 84 MET cc_start: 0.6091 (tpt) cc_final: 0.5777 (tpt) REVERT: F 608 MET cc_start: 0.9050 (mtm) cc_final: 0.8778 (mtp) outliers start: 7 outliers final: 4 residues processed: 236 average time/residue: 0.2089 time to fit residues: 81.3378 Evaluate side-chains 174 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 168 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain E residue 230 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 0.0570 chunk 424 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.114067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.069455 restraints weight = 68958.237| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 3.11 r_work: 0.2699 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 35154 Z= 0.231 Angle : 0.621 8.248 47550 Z= 0.317 Chirality : 0.046 0.148 5364 Planarity : 0.005 0.062 6234 Dihedral : 6.855 58.310 4860 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.52 % Favored : 96.20 % Rotamer: Outliers : 1.72 % Allowed : 12.98 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.14), residues: 4344 helix: 1.09 (0.13), residues: 1836 sheet: -0.23 (0.19), residues: 684 loop : -0.29 (0.17), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 766 TYR 0.011 0.002 TYR D 138 PHE 0.015 0.002 PHE D 506 TRP 0.010 0.002 TRP A 551 HIS 0.005 0.001 HIS C 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.23 (35148) covalent geometry : angle 0.62127 / 0.32 (47550) hydrogen bonds : bond 0.04709 / 3.18 ( 1464) hydrogen bonds : angle 4.67686 / 3.36 ( 4176) Misc. bond : bond 0.00379 / 0.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 183 time to evaluate : 1.425 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.6707 (tpt) cc_final: 0.6135 (tpt) REVERT: A 230 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8446 (t80) REVERT: B 84 MET cc_start: 0.6626 (tpt) cc_final: 0.6283 (tpt) REVERT: B 161 VAL cc_start: 0.7652 (m) cc_final: 0.7386 (m) REVERT: D 84 MET cc_start: 0.6691 (tpt) cc_final: 0.6205 (tpt) REVERT: D 146 ILE cc_start: 0.8290 (mp) cc_final: 0.7944 (mp) REVERT: D 230 PHE cc_start: 0.8869 (OUTLIER) cc_final: 0.8458 (t80) REVERT: E 84 MET cc_start: 0.6736 (tpt) cc_final: 0.6361 (tpt) REVERT: E 152 PHE cc_start: 0.8456 (p90) cc_final: 0.7828 (p90) outliers start: 64 outliers final: 19 residues processed: 238 average time/residue: 0.1784 time to fit residues: 74.1853 Evaluate side-chains 186 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 230 PHE Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 611 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 20 optimal weight: 2.9990 chunk 399 optimal weight: 0.7980 chunk 331 optimal weight: 1.9990 chunk 268 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 378 optimal weight: 0.2980 chunk 27 optimal weight: 0.9990 chunk 263 optimal weight: 4.9990 chunk 415 optimal weight: 1.9990 chunk 327 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.115894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.071819 restraints weight = 68818.972| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 3.22 r_work: 0.2734 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 35154 Z= 0.113 Angle : 0.527 8.373 47550 Z= 0.269 Chirality : 0.042 0.184 5364 Planarity : 0.004 0.056 6234 Dihedral : 6.576 58.827 4856 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.41 % Favored : 96.32 % Rotamer: Outliers : 1.67 % Allowed : 13.09 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.14), residues: 4344 helix: 1.28 (0.13), residues: 1836 sheet: -0.24 (0.20), residues: 660 loop : -0.17 (0.17), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 766 TYR 0.011 0.001 TYR D 138 PHE 0.020 0.001 PHE A 152 TRP 0.007 0.001 TRP F 551 HIS 0.002 0.001 HIS D 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 (35148) covalent geometry : angle 0.52683 / 0.27 (47550) hydrogen bonds : bond 0.03760 / 2.55 ( 1464) hydrogen bonds : angle 4.32050 / 3.11 ( 4176) Misc. bond : bond 0.00121 / 0.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 174 time to evaluate : 1.484 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.6991 (tpt) cc_final: 0.6482 (tpt) REVERT: A 146 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8023 (mp) REVERT: A 230 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.8519 (t80) REVERT: B 84 MET cc_start: 0.6730 (tpt) cc_final: 0.6431 (tpt) REVERT: B 230 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.8643 (m-80) REVERT: B 420 LEU cc_start: 0.9049 (mt) cc_final: 0.8800 (mt) REVERT: B 630 ASP cc_start: 0.8674 (p0) cc_final: 0.8467 (p0) REVERT: C 427 MET cc_start: 0.7728 (ppp) cc_final: 0.6689 (ppp) REVERT: D 84 MET cc_start: 0.6878 (tpt) cc_final: 0.6588 (tpt) REVERT: D 230 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8539 (t80) REVERT: E 60 LYS cc_start: 0.8306 (tptt) cc_final: 0.8085 (tptt) REVERT: E 84 MET cc_start: 0.7035 (tpt) cc_final: 0.6686 (tpt) REVERT: E 152 PHE cc_start: 0.8513 (p90) cc_final: 0.7929 (p90) REVERT: E 230 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.8628 (m-80) REVERT: E 427 MET cc_start: 0.7317 (ppp) cc_final: 0.6575 (ppp) REVERT: F 153 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8441 (tm) REVERT: F 427 MET cc_start: 0.7559 (ppp) cc_final: 0.6584 (ppp) outliers start: 62 outliers final: 21 residues processed: 228 average time/residue: 0.2085 time to fit residues: 81.3706 Evaluate side-chains 191 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 230 PHE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 230 PHE Chi-restraints excluded: chain F residue 611 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 192 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 181 optimal weight: 6.9990 chunk 199 optimal weight: 4.9990 chunk 380 optimal weight: 3.9990 chunk 311 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 371 optimal weight: 10.0000 chunk 356 optimal weight: 0.6980 chunk 313 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 285 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.114552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.069381 restraints weight = 69427.387| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 3.19 r_work: 0.2701 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 35154 Z= 0.185 Angle : 0.558 7.456 47550 Z= 0.283 Chirality : 0.044 0.181 5364 Planarity : 0.004 0.055 6234 Dihedral : 6.597 59.905 4856 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.22 % Favored : 96.50 % Rotamer: Outliers : 2.34 % Allowed : 12.41 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.14), residues: 4344 helix: 1.31 (0.13), residues: 1842 sheet: -0.16 (0.19), residues: 672 loop : -0.26 (0.16), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 766 TYR 0.008 0.001 TYR B 138 PHE 0.014 0.002 PHE A 152 TRP 0.008 0.002 TRP E 551 HIS 0.004 0.001 HIS C 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (35148) covalent geometry : angle 0.55791 / 0.28 (47550) hydrogen bonds : bond 0.03918 / 2.65 ( 1464) hydrogen bonds : angle 4.24421 / 3.05 ( 4176) Misc. bond : bond 0.00077 / 0.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 173 time to evaluate : 1.273 Fit side-chains REVERT: A 84 MET cc_start: 0.6953 (tpt) cc_final: 0.6588 (tpt) REVERT: A 230 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.8569 (t80) REVERT: B 60 LYS cc_start: 0.8351 (tptt) cc_final: 0.8069 (mtmm) REVERT: B 84 MET cc_start: 0.6693 (tpt) cc_final: 0.6476 (tpt) REVERT: B 427 MET cc_start: 0.7515 (ppp) cc_final: 0.6621 (ppp) REVERT: B 630 ASP cc_start: 0.8678 (p0) cc_final: 0.8469 (p0) REVERT: C 427 MET cc_start: 0.7751 (ppp) cc_final: 0.6753 (ppp) REVERT: D 84 MET cc_start: 0.6535 (tpt) cc_final: 0.6103 (tpt) REVERT: D 230 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8539 (t80) REVERT: D 427 MET cc_start: 0.7499 (ppp) cc_final: 0.6756 (ppp) REVERT: E 84 MET cc_start: 0.7048 (tpt) cc_final: 0.6817 (tpt) REVERT: E 152 PHE cc_start: 0.8422 (p90) cc_final: 0.7903 (p90) REVERT: E 427 MET cc_start: 0.7309 (ppp) cc_final: 0.6611 (ppp) REVERT: F 153 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8318 (tm) REVERT: F 427 MET cc_start: 0.7629 (ppp) cc_final: 0.6695 (ppp) REVERT: F 608 MET cc_start: 0.9122 (mtm) cc_final: 0.8858 (mtm) outliers start: 87 outliers final: 39 residues processed: 249 average time/residue: 0.1761 time to fit residues: 77.5060 Evaluate side-chains 208 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 166 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 230 PHE Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 611 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 230 optimal weight: 2.9990 chunk 22 optimal weight: 0.0470 chunk 273 optimal weight: 20.0000 chunk 166 optimal weight: 0.3980 chunk 373 optimal weight: 9.9990 chunk 299 optimal weight: 20.0000 chunk 118 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 343 optimal weight: 0.4980 chunk 318 optimal weight: 4.9990 overall best weight: 1.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 HIS D 115 HIS F 285 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.115077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.070945 restraints weight = 69256.570| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.32 r_work: 0.2698 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 35154 Z= 0.139 Angle : 0.532 7.829 47550 Z= 0.271 Chirality : 0.043 0.188 5364 Planarity : 0.004 0.055 6234 Dihedral : 6.500 59.764 4854 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.36 % Favored : 96.36 % Rotamer: Outliers : 1.67 % Allowed : 12.74 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.14), residues: 4344 helix: 1.39 (0.13), residues: 1842 sheet: -0.11 (0.20), residues: 654 loop : -0.22 (0.16), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 766 TYR 0.010 0.001 TYR D 138 PHE 0.014 0.001 PHE A 152 TRP 0.007 0.002 TRP E 551 HIS 0.003 0.001 HIS C 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (35148) covalent geometry : angle 0.53242 / 0.27 (47550) hydrogen bonds : bond 0.03550 / 2.40 ( 1464) hydrogen bonds : angle 4.12549 / 2.96 ( 4176) Misc. bond : bond 0.00113 / 0.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 164 time to evaluate : 1.352 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.6638 (tpt) cc_final: 0.6217 (tpt) REVERT: A 230 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8469 (t80) REVERT: B 60 LYS cc_start: 0.8548 (tptt) cc_final: 0.7953 (mtmm) REVERT: B 84 MET cc_start: 0.6942 (tpt) cc_final: 0.6541 (tpt) REVERT: B 427 MET cc_start: 0.7488 (ppp) cc_final: 0.6632 (ppp) REVERT: B 630 ASP cc_start: 0.8611 (p0) cc_final: 0.8407 (p0) REVERT: C 66 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7556 (mm-30) REVERT: C 427 MET cc_start: 0.7727 (ppp) cc_final: 0.6758 (ppp) REVERT: C 608 MET cc_start: 0.9213 (OUTLIER) cc_final: 0.8812 (mtm) REVERT: D 84 MET cc_start: 0.6478 (tpt) cc_final: 0.6023 (tpt) REVERT: D 230 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8439 (t80) REVERT: D 427 MET cc_start: 0.7499 (ppp) cc_final: 0.6792 (ppp) REVERT: E 60 LYS cc_start: 0.8319 (tptt) cc_final: 0.7900 (mtmm) REVERT: E 84 MET cc_start: 0.7067 (tpt) cc_final: 0.6754 (tpt) REVERT: E 152 PHE cc_start: 0.8473 (p90) cc_final: 0.8018 (p90) REVERT: E 427 MET cc_start: 0.7298 (ppp) cc_final: 0.6629 (ppp) REVERT: F 153 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8412 (tm) REVERT: F 427 MET cc_start: 0.7603 (ppp) cc_final: 0.6668 (ppp) outliers start: 62 outliers final: 37 residues processed: 217 average time/residue: 0.1882 time to fit residues: 72.0028 Evaluate side-chains 202 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 160 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 608 MET Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 230 PHE Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 611 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 10 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 313 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 159 optimal weight: 0.0170 chunk 418 optimal weight: 4.9990 chunk 258 optimal weight: 8.9990 chunk 409 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 163 optimal weight: 0.6980 overall best weight: 1.5424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 285 ASN E 285 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.114391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.070426 restraints weight = 69237.062| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 3.29 r_work: 0.2697 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 35154 Z= 0.147 Angle : 0.530 8.924 47550 Z= 0.269 Chirality : 0.043 0.151 5364 Planarity : 0.004 0.055 6234 Dihedral : 6.453 59.830 4854 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.73 % Favored : 96.06 % Rotamer: Outliers : 1.59 % Allowed : 12.92 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.14), residues: 4344 helix: 1.43 (0.13), residues: 1842 sheet: -0.07 (0.20), residues: 654 loop : -0.18 (0.16), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 766 TYR 0.010 0.001 TYR E 138 PHE 0.013 0.001 PHE D 131 TRP 0.006 0.002 TRP E 551 HIS 0.003 0.001 HIS C 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (35148) covalent geometry : angle 0.52998 / 0.27 (47550) hydrogen bonds : bond 0.03510 / 2.37 ( 1464) hydrogen bonds : angle 4.06457 / 2.92 ( 4176) Misc. bond : bond 0.00142 / 0.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 162 time to evaluate : 1.054 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.6749 (tpt) cc_final: 0.6413 (tpt) REVERT: A 230 PHE cc_start: 0.8922 (OUTLIER) cc_final: 0.8521 (t80) REVERT: A 427 MET cc_start: 0.7506 (ppp) cc_final: 0.6741 (ppp) REVERT: B 84 MET cc_start: 0.7165 (tpt) cc_final: 0.6864 (tpt) REVERT: B 427 MET cc_start: 0.7491 (ppp) cc_final: 0.6733 (ppp) REVERT: B 630 ASP cc_start: 0.8606 (p0) cc_final: 0.8404 (p0) REVERT: C 66 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7515 (mm-30) REVERT: C 427 MET cc_start: 0.7794 (ppp) cc_final: 0.6845 (ppp) REVERT: C 608 MET cc_start: 0.9209 (OUTLIER) cc_final: 0.8930 (mtm) REVERT: D 84 MET cc_start: 0.6661 (tpt) cc_final: 0.6304 (tpt) REVERT: D 159 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7780 (ptm-80) REVERT: D 230 PHE cc_start: 0.8883 (OUTLIER) cc_final: 0.8546 (t80) REVERT: D 427 MET cc_start: 0.7522 (ppp) cc_final: 0.6813 (ppp) REVERT: E 84 MET cc_start: 0.7296 (tpt) cc_final: 0.6984 (tpt) REVERT: E 152 PHE cc_start: 0.8653 (p90) cc_final: 0.8210 (p90) REVERT: E 427 MET cc_start: 0.7317 (ppp) cc_final: 0.6653 (ppp) REVERT: F 153 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8480 (tm) REVERT: F 427 MET cc_start: 0.7685 (ppp) cc_final: 0.6794 (ppp) REVERT: F 608 MET cc_start: 0.9103 (mtm) cc_final: 0.8861 (mtm) outliers start: 59 outliers final: 40 residues processed: 214 average time/residue: 0.1913 time to fit residues: 71.7126 Evaluate side-chains 204 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 158 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 608 MET Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 611 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 39 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 410 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 143 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 383 optimal weight: 0.7980 chunk 347 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 HIS B 327 GLN E 327 GLN F 327 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.112970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.067999 restraints weight = 69222.148| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 3.17 r_work: 0.2655 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 35154 Z= 0.209 Angle : 0.575 9.651 47550 Z= 0.291 Chirality : 0.045 0.149 5364 Planarity : 0.005 0.065 6234 Dihedral : 6.564 59.833 4854 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.64 % Favored : 96.22 % Rotamer: Outliers : 1.51 % Allowed : 13.35 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.14), residues: 4344 helix: 1.39 (0.13), residues: 1842 sheet: -0.09 (0.20), residues: 672 loop : -0.22 (0.16), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 766 TYR 0.012 0.001 TYR D 138 PHE 0.015 0.002 PHE C 506 TRP 0.009 0.002 TRP E 551 HIS 0.004 0.001 HIS F 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.21 (35148) covalent geometry : angle 0.57451 / 0.29 (47550) hydrogen bonds : bond 0.03871 / 2.61 ( 1464) hydrogen bonds : angle 4.09838 / 2.94 ( 4176) Misc. bond : bond 0.00182 / 0.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 160 time to evaluate : 1.346 Fit side-chains revert: symmetry clash REVERT: A 84 MET cc_start: 0.6701 (tpt) cc_final: 0.6333 (tpt) REVERT: A 230 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.8457 (t80) REVERT: B 84 MET cc_start: 0.6869 (tpt) cc_final: 0.6593 (tpt) REVERT: B 152 PHE cc_start: 0.8465 (p90) cc_final: 0.8254 (p90) REVERT: B 427 MET cc_start: 0.7521 (ppp) cc_final: 0.6769 (ppp) REVERT: B 550 MET cc_start: 0.7880 (ttp) cc_final: 0.7172 (tmm) REVERT: B 630 ASP cc_start: 0.8691 (p0) cc_final: 0.8452 (p0) REVERT: C 66 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7450 (mm-30) REVERT: C 427 MET cc_start: 0.7723 (ppp) cc_final: 0.6772 (ppp) REVERT: C 608 MET cc_start: 0.9223 (OUTLIER) cc_final: 0.8828 (mtm) REVERT: D 230 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8600 (t80) REVERT: D 427 MET cc_start: 0.7611 (ppp) cc_final: 0.6914 (ppp) REVERT: E 60 LYS cc_start: 0.8290 (tptt) cc_final: 0.8000 (mtmm) REVERT: E 84 MET cc_start: 0.6802 (tpt) cc_final: 0.6506 (tpt) REVERT: E 152 PHE cc_start: 0.8506 (p90) cc_final: 0.8137 (p90) REVERT: E 427 MET cc_start: 0.7292 (ppp) cc_final: 0.6615 (ppp) REVERT: F 153 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8427 (tm) REVERT: F 427 MET cc_start: 0.7639 (ppp) cc_final: 0.6759 (ppp) outliers start: 56 outliers final: 40 residues processed: 209 average time/residue: 0.1882 time to fit residues: 68.3416 Evaluate side-chains 197 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 152 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 608 MET Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 611 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 346 optimal weight: 2.9990 chunk 226 optimal weight: 9.9990 chunk 284 optimal weight: 0.0000 chunk 322 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 315 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 232 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 252 optimal weight: 6.9990 overall best weight: 2.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.113491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.068583 restraints weight = 69440.070| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 3.09 r_work: 0.2661 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 35154 Z= 0.194 Angle : 0.568 12.647 47550 Z= 0.287 Chirality : 0.044 0.142 5364 Planarity : 0.004 0.059 6234 Dihedral : 6.567 59.801 4854 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.78 % Favored : 96.09 % Rotamer: Outliers : 1.59 % Allowed : 13.49 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.14), residues: 4344 helix: 1.38 (0.13), residues: 1842 sheet: -0.09 (0.20), residues: 654 loop : -0.20 (0.16), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 766 TYR 0.010 0.001 TYR E 138 PHE 0.026 0.002 PHE D 152 TRP 0.009 0.002 TRP E 551 HIS 0.003 0.001 HIS B 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.19 (35148) covalent geometry : angle 0.56842 / 0.29 (47550) hydrogen bonds : bond 0.03729 / 2.52 ( 1464) hydrogen bonds : angle 4.06097 / 2.91 ( 4176) Misc. bond : bond 0.00124 / 0.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 161 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.6914 (tpt) cc_final: 0.6666 (tpt) REVERT: B 114 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8393 (mp) REVERT: B 152 PHE cc_start: 0.8613 (p90) cc_final: 0.8389 (p90) REVERT: B 427 MET cc_start: 0.7557 (ppp) cc_final: 0.6828 (ppp) REVERT: B 550 MET cc_start: 0.7965 (ttp) cc_final: 0.7102 (tmm) REVERT: B 630 ASP cc_start: 0.8706 (p0) cc_final: 0.8459 (p0) REVERT: C 66 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7485 (mm-30) REVERT: C 427 MET cc_start: 0.7716 (ppp) cc_final: 0.6754 (ppp) REVERT: C 473 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8662 (mm-40) REVERT: C 608 MET cc_start: 0.9223 (OUTLIER) cc_final: 0.8821 (mtm) REVERT: D 84 MET cc_start: 0.7026 (tpt) cc_final: 0.6568 (tpt) REVERT: D 230 PHE cc_start: 0.8913 (OUTLIER) cc_final: 0.8527 (t80) REVERT: D 427 MET cc_start: 0.7630 (ppp) cc_final: 0.6971 (ppp) REVERT: E 152 PHE cc_start: 0.8655 (p90) cc_final: 0.8241 (p90) REVERT: E 427 MET cc_start: 0.7345 (ppp) cc_final: 0.6665 (ppp) REVERT: F 153 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8532 (tm) REVERT: F 427 MET cc_start: 0.7686 (ppp) cc_final: 0.6828 (ppp) outliers start: 59 outliers final: 43 residues processed: 210 average time/residue: 0.1851 time to fit residues: 67.2597 Evaluate side-chains 206 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 157 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 473 GLN Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 608 MET Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 611 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 304 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 chunk 165 optimal weight: 0.6980 chunk 84 optimal weight: 30.0000 chunk 255 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 297 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 376 optimal weight: 0.0070 chunk 187 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 overall best weight: 1.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.114199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.069355 restraints weight = 69206.800| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 3.10 r_work: 0.2684 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 35154 Z= 0.147 Angle : 0.543 10.885 47550 Z= 0.274 Chirality : 0.043 0.142 5364 Planarity : 0.004 0.055 6234 Dihedral : 6.482 59.910 4854 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.82 % Favored : 96.04 % Rotamer: Outliers : 1.43 % Allowed : 13.68 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.14), residues: 4344 helix: 1.45 (0.13), residues: 1860 sheet: -0.10 (0.20), residues: 654 loop : -0.21 (0.16), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 766 TYR 0.011 0.001 TYR E 138 PHE 0.022 0.001 PHE D 152 TRP 0.007 0.002 TRP E 551 HIS 0.003 0.001 HIS E 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (35148) covalent geometry : angle 0.54302 / 0.27 (47550) hydrogen bonds : bond 0.03455 / 2.33 ( 1464) hydrogen bonds : angle 3.99261 / 2.85 ( 4176) Misc. bond : bond 0.00092 / 0.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 158 time to evaluate : 2.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.6911 (tpt) cc_final: 0.6696 (tpp) REVERT: A 427 MET cc_start: 0.7557 (ppp) cc_final: 0.6782 (ppp) REVERT: B 152 PHE cc_start: 0.8543 (p90) cc_final: 0.8343 (p90) REVERT: B 427 MET cc_start: 0.7527 (ppp) cc_final: 0.6820 (ppp) REVERT: B 550 MET cc_start: 0.7916 (ttp) cc_final: 0.7714 (ttm) REVERT: B 630 ASP cc_start: 0.8659 (p0) cc_final: 0.8430 (p0) REVERT: B 678 MET cc_start: 0.9099 (mmm) cc_final: 0.8891 (mmm) REVERT: C 66 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7478 (mm-30) REVERT: C 427 MET cc_start: 0.7667 (ppp) cc_final: 0.6751 (ppp) REVERT: C 473 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8623 (mm-40) REVERT: C 608 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8797 (mtm) REVERT: D 230 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.8459 (t80) REVERT: D 427 MET cc_start: 0.7618 (ppp) cc_final: 0.6961 (ppp) REVERT: D 550 MET cc_start: 0.7840 (ttp) cc_final: 0.7453 (ttm) REVERT: E 152 PHE cc_start: 0.8593 (p90) cc_final: 0.8316 (p90) REVERT: E 427 MET cc_start: 0.7313 (ppp) cc_final: 0.6643 (ppp) REVERT: F 153 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8518 (tm) REVERT: F 427 MET cc_start: 0.7625 (ppp) cc_final: 0.6781 (ppp) outliers start: 53 outliers final: 42 residues processed: 204 average time/residue: 0.1858 time to fit residues: 66.7526 Evaluate side-chains 198 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 151 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 473 GLN Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 608 MET Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 611 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 118 optimal weight: 5.9990 chunk 407 optimal weight: 4.9990 chunk 206 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 233 optimal weight: 3.9990 chunk 170 optimal weight: 0.7980 chunk 329 optimal weight: 30.0000 chunk 246 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 360 optimal weight: 9.9990 chunk 358 optimal weight: 7.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 HIS D 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.113160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.067782 restraints weight = 69563.698| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 3.26 r_work: 0.2649 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 35154 Z= 0.193 Angle : 0.570 10.806 47550 Z= 0.287 Chirality : 0.044 0.161 5364 Planarity : 0.004 0.064 6234 Dihedral : 6.530 59.945 4854 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.82 % Favored : 96.04 % Rotamer: Outliers : 1.35 % Allowed : 13.79 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.14), residues: 4344 helix: 1.44 (0.13), residues: 1860 sheet: -0.11 (0.20), residues: 654 loop : -0.23 (0.16), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 766 TYR 0.009 0.001 TYR E 138 PHE 0.038 0.002 PHE A 363 TRP 0.009 0.002 TRP E 551 HIS 0.003 0.001 HIS D 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.19 (35148) covalent geometry : angle 0.57042 / 0.29 (47550) hydrogen bonds : bond 0.03719 / 2.51 ( 1464) hydrogen bonds : angle 4.01605 / 2.87 ( 4176) Misc. bond : bond 0.00126 / 0.06 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 152 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.6941 (tpt) cc_final: 0.6722 (tpp) REVERT: A 427 MET cc_start: 0.7535 (ppp) cc_final: 0.6900 (ppp) REVERT: B 84 MET cc_start: 0.6329 (tpt) cc_final: 0.5936 (tpt) REVERT: B 427 MET cc_start: 0.7533 (ppp) cc_final: 0.6835 (ppp) REVERT: B 630 ASP cc_start: 0.8696 (p0) cc_final: 0.8451 (p0) REVERT: B 678 MET cc_start: 0.9092 (mmm) cc_final: 0.8869 (mmm) REVERT: C 66 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7418 (mm-30) REVERT: C 427 MET cc_start: 0.7660 (ppp) cc_final: 0.6752 (ppp) REVERT: C 473 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8650 (mm-40) REVERT: C 608 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8816 (mtm) REVERT: D 84 MET cc_start: 0.6564 (tpt) cc_final: 0.6084 (tpt) REVERT: D 230 PHE cc_start: 0.8847 (OUTLIER) cc_final: 0.8370 (t80) REVERT: D 427 MET cc_start: 0.7608 (ppp) cc_final: 0.6948 (ppp) REVERT: D 550 MET cc_start: 0.7877 (ttp) cc_final: 0.7516 (ttm) REVERT: E 152 PHE cc_start: 0.8487 (p90) cc_final: 0.8243 (p90) REVERT: E 427 MET cc_start: 0.7331 (ppp) cc_final: 0.6655 (ppp) REVERT: F 153 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8467 (tm) REVERT: F 427 MET cc_start: 0.7685 (ppp) cc_final: 0.6848 (ppp) outliers start: 50 outliers final: 42 residues processed: 194 average time/residue: 0.1929 time to fit residues: 65.2184 Evaluate side-chains 194 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 147 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 230 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain C residue 473 GLN Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 608 MET Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 611 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 287 optimal weight: 2.9990 chunk 329 optimal weight: 0.8980 chunk 147 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 338 optimal weight: 0.9980 chunk 394 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 386 optimal weight: 0.7980 chunk 163 optimal weight: 0.8980 chunk 133 optimal weight: 0.0000 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 HIS B 558 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.114875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.070973 restraints weight = 68970.200| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.29 r_work: 0.2717 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 35154 Z= 0.106 Angle : 0.519 11.263 47550 Z= 0.260 Chirality : 0.043 0.161 5364 Planarity : 0.004 0.056 6234 Dihedral : 6.351 59.535 4854 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.98 % Favored : 95.88 % Rotamer: Outliers : 1.13 % Allowed : 14.11 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.14), residues: 4344 helix: 1.60 (0.13), residues: 1842 sheet: -0.25 (0.20), residues: 672 loop : -0.14 (0.16), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 766 TYR 0.010 0.001 TYR E 138 PHE 0.023 0.001 PHE B 152 TRP 0.006 0.001 TRP C 454 HIS 0.002 0.000 HIS D 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (35148) covalent geometry : angle 0.51879 / 0.26 (47550) hydrogen bonds : bond 0.03098 / 2.09 ( 1464) hydrogen bonds : angle 3.91594 / 2.79 ( 4176) Misc. bond : bond 0.00024 / 0.01 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7957.17 seconds wall clock time: 137 minutes 11.93 seconds (8231.93 seconds total)